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Merge pull request #1368 from Libensemble/release/v_1.4.0
Release/v 1.4.0
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‎.codecov.yml‎

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ignore:
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- "libensemble/tools/parse_args.py"
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- "libensemble/tools/forkable_pdb.py"
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- "libensemble/tools/live_data/*"
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- "libensemble/sim_funcs/executor_hworld.py"
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- "libensemble/gen_funcs/persistent_ax_multitask.py"
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- "libensemble/gen_funcs/persistent_gpCAM.py"

‎.flake8‎

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libensemble/tests/functionality_tests/test_stats_output.py:E402
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libensemble/tests/functionality_tests/test_active_persistent_worker_abort.py:E402
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libensemble/tests/unit_tests/test_persistent_aposmm.py:E402
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libensemble/tests/unit_tests/RENAME_test_persistent_aposmm.py:E402
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# Allow undefined name '__version__'
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setup.py:F821

‎.github/workflows/basic.yml‎

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include:
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- os: macos-latest
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python-version: "3.11"
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mpi-version: "mpich=4.2.1"
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mpi-version: mpich
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pydantic-version: "2.6.4"
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comms-type: m
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- os: macos-latest
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python-version: "3.11"
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mpi-version: "mpich=4.2.1"
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mpi-version: mpich
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pydantic-version: "2.6.4"
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comms-type: l
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- os: ubuntu-latest
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v4
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- uses: crate-ci/typos@v1.20.10
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- uses: crate-ci/typos@v1.23.3

‎.github/workflows/extra.yml‎

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include:
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- os: macos-latest
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python-version: 3.11
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mpi-version: "mpich=4.2.0"
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mpi-version: mpich
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pydantic-version: "2.6.4"
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comms-type: m
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- os: macos-latest
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python-version: 3.11
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mpi-version: "mpich=4.2.0"
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mpi-version: mpich
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pydantic-version: "2.6.4"
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comms-type: l
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- os: ubuntu-latest
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python-version: "3.10"
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mpi-version: "mpich"
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mpi-version: mpich
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pydantic-version: "2.6.4"
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comms-type: t
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- os: ubuntu-latest
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- name: Install generator dependencies
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run: |
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python -m pip install --upgrade pip
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pip install mpmath matplotlib ax-platform
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pip install mpmath
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pip install matplotlib
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conda env update --file install/gen_deps_environment.yml
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- name: Install ax-platform
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run: |
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pip install ax-platform
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#- name: Install ax-platform
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# run: pip install "ax-platform<=0.4.0"
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- name: Install gpcam
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if: matrix.python-version != '3.12'
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if: matrix.python-version >= '3.11'
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run: |
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rm ./libensemble/tests/regression_tests/test_ytopt_heffte.py
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rm ./libensemble/tests/regression_tests/test_gpCAM.py
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# rm ./libensemble/tests/regression_tests/test_gpCAM.py
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rm ./libensemble/tests/regression_tests/test_persistent_gp.py
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- name: Remove test for persistent Tasmanian on Python 3.12
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v4
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- uses: crate-ci/typos@v1.20.10
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- uses: crate-ci/typos@v1.23.3

‎.wci.yml‎

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language: Python
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release:
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version: 1.3.0
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date: 2024-05-01
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version: 1.4.0
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date: 2024-07-25
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documentation:
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general: https://libensemble.readthedocs.io

‎CHANGELOG.rst‎

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.. _`github releases page`: https://github.com/Libensemble/libensemble/releases
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Release 1.4.0
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--------------
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:Date: July 25, 2024
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* Add a ``live_data`` option for real-time data collection / plotting. #1310
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* ``nworkers``/``is_manager`` are set when ``Ensemble`` object is created. #1331/ #1336
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* This update locks the comms method when ``Ensemble`` object is created.
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* Add a ``group_size`` option to deal with unevenly resourced nodes. #1349
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* Bug fix: Fix shutdown hang on worker error when using ``gen_on_manager``. #1348
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* Bug fix: Log level was locked to ``INFO`` when using class interface.
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* Updated code to support ``numpy`` 2.0.
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Documentation:
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* Notebook examples with Colab links added to documentation. #1310
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* E.g., https://colab.research.google.com/github/Libensemble/libensemble/blob/develop/examples/tutorials/aposmm/aposmm_tutorial_notebook.ipynb
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* Example of templating input files added to forces tutorial. #1310
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Example user functions:
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* Update ``gpCAM`` generators to work with latest interface.
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* Change ``one_d_func`` to ``norm_eval``. Works with multiple dimensions. #1352 / #1354
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:Note:
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* Tests were run on Linux and MacOS with Python versions 3.9, 3.10, 3.11, 3.12
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* Heterogeneous workflows tested on Frontier (OLCF), Polaris (ALCF), and Perlmutter (NERSC).
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* Note that tests have been recently run on Aurora (ALCF), but the system was unavailable at time of release.
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* Tests were also run on Bebop and Improv LCRC systems.
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:Known Issues:
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* See known issues section in the documentation.
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Release 1.3.0
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--------------
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‎README.rst‎

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===========
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Create an ``Ensemble``, then customize it with general settings, simulation and generator parameters,
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and an exit condition. Run the following via ``python this_file.py --comms local --nworkers 4``:
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and an exit condition. Run the following four-worker example via ``python this_file.py``:
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.. code-block:: python
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import numpy as np
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from libensemble import Ensemble
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from libensemble.gen_funcs.sampling import uniform_random_sample
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from libensemble.sim_funcs.six_hump_camel import six_hump_camel
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from libensemble.specs import ExitCriteria, GenSpecs, SimSpecs
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from libensemble.tools import add_unique_random_streams
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if __name__ == "__main__":
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sampling = Ensemble(parse_args=True)
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sampling.sim_specs = SimSpecs(
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sim_f=six_hump_camel,
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inputs=["x"],
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outputs=[("f", float)],
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)
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sampling.gen_specs = GenSpecs(
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gen_f=uniform_random_sample,
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outputs=[("x", float, (2,))],
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user={
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"gen_batch_size": 500,
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"lb": np.array([-3, -2]),
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"ub": np.array([3, 2]),
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},
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)
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sampling.persis_info = add_unique_random_streams({}, sampling.nworkers + 1)
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sampling.exit_criteria = ExitCriteria(sim_max=101)
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sampling.run()
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sampling.save_output(__file__)
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if sampling.is_manager:
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print("Some output data:\n", sampling.H[["x", "f"]][:10])
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import numpy as np
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from libensemble import Ensemble
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from libensemble.gen_funcs.sampling import uniform_random_sample
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from libensemble.sim_funcs.six_hump_camel import six_hump_camel
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from libensemble.specs import ExitCriteria, GenSpecs, LibeSpecs, SimSpecs
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if __name__ == "__main__":
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libE_specs = LibeSpecs(nworkers=4)
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sim_specs = SimSpecs(
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sim_f=six_hump_camel,
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inputs=["x"],
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outputs=[("f", float)],
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)
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gen_specs = GenSpecs(
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gen_f=uniform_random_sample,
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outputs=[("x", float, (2,))],
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user={
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"gen_batch_size": 50,
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"lb": np.array([-3, -2]),
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"ub": np.array([3, 2]),
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},
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)
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exit_criteria = ExitCriteria(sim_max=100)
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sampling = Ensemble(
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libE_specs=libE_specs,
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sim_specs=sim_specs,
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gen_specs=gen_specs,
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exit_criteria=exit_criteria,
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)
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sampling.add_random_streams()
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sampling.run()
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if sampling.is_manager:
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sampling.save_output(__file__)
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print("Some output data:\n", sampling.H[["x", "f"]][:10])
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|Inline Example|
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Try some other examples live in Colab.
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+---------------------------------------------------------------+-------------------------------------+
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| Description | Try online |
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+===============================================================+=====================================+
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| Simple Ensemble that makes a Sine wave. | |Simple Ensemble| |
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+---------------------------------------------------------------+-------------------------------------+
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| Ensemble with an MPI application. | |Ensemble with an MPI application| |
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+---------------------------------------------------------------+-------------------------------------+
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| Optimization example that finds multiple minima. | |Optimization example| |
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+---------------------------------------------------------------+-------------------------------------+
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There are many more examples in the `regression tests`_.
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Resources
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=========
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.. _PyPI: https://pypi.org
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.. _Quickstart: https://libensemble.readthedocs.io/en/main/introduction.html
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.. _ReadtheDocs: http://libensemble.readthedocs.org/
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.. _regression tests: https://github.com/Libensemble/libensemble/tree/main/libensemble/tests/regression_tests
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.. |Inline Example| image:: https://colab.research.google.com/assets/colab-badge.svg
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:target: http://colab.research.google.com/github/Libensemble/libensemble/blob/develop/examples/readme_notebook.ipynb
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.. |Simple Ensemble| image:: https://colab.research.google.com/assets/colab-badge.svg
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:target: http://colab.research.google.com/github/Libensemble/libensemble/blob/develop/examples/tutorials/simple_sine/sine_tutorial_notebook.ipynb
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.. |Ensemble with an MPI application| image:: https://colab.research.google.com/assets/colab-badge.svg
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:target: http://colab.research.google.com/github/Libensemble/libensemble/blob/develop/examples/tutorials/forces_with_executor/forces_tutorial_notebook.ipynb
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.. |Optimization example| image:: https://colab.research.google.com/assets/colab-badge.svg
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:target: http://colab.research.google.com/github/Libensemble/libensemble/blob/develop/examples/tutorials/aposmm/aposmm_tutorial_notebook.ipynb

‎docs/FAQ.rst‎

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logger.set_level("DEBUG")
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libE_specs["safe_mode"] = True
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To make it easier to debug a generator try setting the **libE_specs** option ``gen_on_manager``.
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To do so, add the following to your calling script::
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libE_specs["gen_on_manager"] = True
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With this, ``pdb`` breakpoints can be set as usual in the generator.
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For more debugging options see "How can I debug specific libEnsemble processes?" below.
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Common Errors
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-------------
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‎docs/advanced_installation.rst‎

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* Balsam_ - Manage and submit applications to the Balsam service with our :ref:`BalsamExecutor<balsam-exctr>`
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* pyyaml_ and tomli_ - Parameterize libEnsemble via yaml or toml
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* `Globus Compute`_ - Submit simulation or generator function instances to remote Globus Compute endpoints
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* `psi-j-python`_ and `tqdm`_ - Use `liberegister` and `libesubmit` to submit libEnsemble jobs to any scheduler
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.. _Balsam: https://balsam.readthedocs.io/en/latest/
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.. _conda-forge: https://conda-forge.org/
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.. _MPICH: https://www.mpich.org/
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.. _NumPy: http://www.numpy.org
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.. _Open MPI: https://www.open-mpi.org/
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.. _psi-j-python: https://github.com/ExaWorks/psi-j-python
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.. _psutil: https://pypi.org/project/psutil/
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.. _pydantic: https://docs.pydantic.dev/1.10/
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.. _PyPI: https://pypi.org

‎docs/conf.py‎

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MOCK_MODULES = [
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"argparse",
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"dfols",
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"IPython",
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"IPython.display",
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"IPython.core",
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"IPython.core.pylabtools",
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"math",
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"matplotlib",
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"matplotlib.pyplot",
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"mpi4py",
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"mpmath",
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"nlopt",
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sys.path.append(os.path.abspath("../libensemble/comms"))
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sys.path.append(os.path.abspath("../libensemble/utils"))
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sys.path.append(os.path.abspath("../libensemble/tools"))
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sys.path.append(os.path.abspath("../libensemble/tools/live_data"))
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sys.path.append(os.path.abspath("../libensemble/executors"))
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sys.path.append(os.path.abspath("../libensemble/resources"))
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# print(sys.path)

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